BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716317.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,896,383 number of mapped reads = 1,745,754 (92.06%) number of supplementary alignments = 33,078 (1.74%) number of secondary alignments = 0 number of mapped bases = 137,696,204 bp number of sequenced bases = 137,632,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,714 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6701 >>>>>>> ACTG content number of A's = 35,976,860 bp (26.14%) number of C's = 26,641,711 bp (19.36%) number of T's = 42,579,927 bp (30.94%) number of G's = 32,424,910 bp (23.56%) number of N's = 9,359 bp (0.01%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 933,873 number of insertions = 11,768 mapped reads with insertion percentage = 0.66% number of deletions = 33,090 mapped reads with deletion percentage = 1.87% homopolymer indels = 42.26% >>>>>>> Coverage mean coverageData = 0.0445X std coverageData = 0.3715X There is a 3.82% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10676363 0.04283384714215015 0.6361257377150156 chr2 243199373 11253713 0.046273610253098806 0.45029231575061524 chr3 198022430 9298600 0.046957306806102724 0.2427304349618487 chr4 191154276 8911684 0.04662037484319734 0.3080872040964425 chr5 180915260 8453688 0.04672733521760409 0.2458833964344202 chr6 171115067 8071571 0.04717042830600066 0.26671463425849823 chr7 159138663 7613033 0.04783899057892676 0.521406213138785 chr8 146364022 6979631 0.047686794231440295 0.461767254782247 chr9 141213431 5759998 0.04078930707377261 0.3326794469462829 chr10 135534747 6541151 0.04826180108632955 0.38699236172472595 chr11 135006516 6384302 0.04728884345108202 0.35162615305061606 chr12 133851895 6265084 0.0468060911651643 0.24462529151030196 chr13 115169878 4398559 0.03819192202322208 0.2188031786381531 chr14 107349540 4182064 0.03895744686004244 0.238870189472682 chr15 102531392 4060103 0.03959863336294118 0.22441115762180425 chr16 90354753 4036021 0.044668607527486685 0.2570095650871672 chr17 81195210 3743776 0.046108335701083844 0.27608049343971974 chr18 78077248 3779813 0.04841119656266573 0.5252638505793201 chr19 59128983 2690650 0.04550475694804357 0.45286100234137755 chr20 63025520 3003301 0.04765214154520264 0.2595321982887542 chr21 48129895 1846581 0.038366611853194364 0.25405953261604614 chr22 51304566 1626881 0.03171025752366758 0.201157598148735 chrMT 16571 12887 0.7776839056182487 1.2490319284098388 chrX 155270560 7702425 0.049606474015421856 0.29686302197306574 chrY 59373566 404325 0.006809848679124309 0.23327735336555186